there are two kinds of tools:

the ones that force you to adapt to how they work, at the cost of limiting what you can do

the ones that adapt to the way you work, at the cost of letting you shoot yourself in the foot

making /obsidian • writing stephango.com

brilliantly put — this era belongs to the second one

The first can be very helpful, limits can create novel solutions. 

The second allows for going as far as you can take it, but as you say, the results can have unintended consequences.

Many tools have aspects of both of course.

The 2nd is the best to me 
Expressing yourself to the maximum is the undisputed best way to deliver optimum efficiency , even if you end up shooting yourself in the foot, at least you can learn and also enjoy every bit of the learning process

My employer chooses the first, I choose the second.